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Dr Julian Marchesi  -  PhD

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Link to ScopusTM Database

Selected Publications:


Lewis DA, Brown R, Williams J, White P, Jacobson SK, Marchesi JR, Drake MJ. The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol. 2013 Aug 15;3:41. doi: 10.3389/fcimb.2013.00041. PMID: 23967406

Prorok-Hamon M, Friswell MK, Alswied A, Roberts CL, Song F, Flanagan PK, Knight P, Codling C, Marchesi JR, Winstanley C, Hall N, Rhodes JM, Campbell BJ. Colonic mucosa-associated diffusely adherent afaC+ Escherichia coli expressing lpfA and pks are increased in inflammatory bowel disease and colon cancer. Gut. 2013 Jul 11. [Epub ahead of print] PMID: 23846483

van Woerden HC, Gregory C, Brown R, Marchesi JR, Hoogendoorn B, Matthews IP. Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study. BMC Infect Dis. 2013 Feb 5;13:69. doi: 10.1186/1471-2334-13-69. PMID: 23384395


Morris LS, Evans J, Marchesi JR. A robust plate assay for detection of extracellular microbial protease activity in metagenomic screens and pure cultures. J. Microbiol. Methods. 2012, 91(1):144-146

Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, Harris HM, Coakley M, Lakshminarayanan B, O'Sullivan O, Fitzgerald GF, Deane J, O'Connor M, Harnedy N, O'Connor K, O'Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi JR, Fitzgerald AP, Shanahan F, Hill C, Ross RP, O'Toole PW. Diet drives gut microbiota variation in the elderly which correlates with health. Nature. 2012, 9;488(7410):178-84

Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, Kerr C, Hourihane J, Murray D, Fuligni F, Gueimonde M, Margolles A, De Bellis G, O'Toole PW, van Sinderen D, Marchesi JR, Ventura M. Diversity of bifidobacteria within the infant gut microbiota. PLoS ONE, 2012, 7(5):e36957

Bull MJ, Marchesi JR, Vandamme P, Plummer S, Mahenthiralingam E. Minimum taxonomic criteria for bacterial genome sequence depositions and announcements. J. Microbiol Methods. 2012, 89:18-21

Culligan E, Sleator R, Marchesi JR and Hill C. Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome. ISME J. 2012, 6(10):1916-25


Li JV, Reshat R, Wu Q, Ashrafian H, Bueter M, le Roux CW, Darzi A, Athanasiou T, Marchesi JR, Nicholson JK1,2, Elaine Holmes E, Gooderham N. Experimental Bariatric Surgery in Rats generates a cytotoxic chemical environment in the gut content. Frontiers in Microbiology. 2011; 2:183.

Brown R, Marchesi JR and Morby A. Functional characterisation of Lp_2714, an EAL-domain protein from Lactobacillus plantarum. Biochemical and Biophysical Research Communications. 2011; 411(1):132-136.

Marchesi JR. Human distal gut microbiome. Env. Microbiol. 2011; 13(12):3088-3102.

Marchesi JR. Shifting from a gene-centric to metabolite-centric strategy to determine the core gut microbiome. Bioengineered Bugs Commentary. 2011; 2(6):309-314.

Li JV, Ashrafian H, Bueter M, Kinross J, Sands C, le Roux CW, Bloom SR, Darzi A, Athanasiou T, Marchesi JR, Nicholson JK and Elaine Holmes E Metabolic Surgery Profoundly Influences Gut Microbial-Host Metabolic Crosstalk. Gut. 2011; 60(9):1214-1223.

Twomey K, de Eulate A, Marchesi JR., Kolida S, Gibson G, Arrigan DWM, Ogurtsov VI. Characterisation of the electrochemical behavior of gastrointestinal fluids using a multi-electrode sensor probe. IEEE Transactions on Biomedical Engineering. 2011; 58(9):2521-2527.

Marchesi JR, Dutilh B, Hall N, Peters W, Roelofs R , Boleij A and Tjalsma H. Towards the Human Colorectal Cancer Tumour Microbiome. PloS ONE. 2011; 6(5):e20447

Swann J, Richards SE, Shen Q, Holmes E, Marchesi JR and Tuohy K. Culture independent analysis of the human gut microbiota and its activities. Molecular Microbial Ecology Manual. 2011

Lejon D, Kennedy J, Marchesi JR and Dobson A. Identification of Novel Bioactive Compounds from the Metagenome of the Marine Sponge Haliclona simulans. Handbook of Molecular Microbial Ecology II:  Metagenomics in Different Habitats, ISBN: 978-0-470-64719-6 2011, Wiley-Blackwell


Marchesi JR. Prokaryotic and eukaryotic diversity of the human gut. . Adv Appl Microbiol. 2010;72:43-62. Review

Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O'Connor M, Harnedy N, O'Connor K, Henry C, O'Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O'Toole PW. Microbes and Health Sackler Colloquium: Composition, variability, and temporal stability of the intestinal microbiota of the elderly.  Proc Natl Acad Sci U S A. 2010 Aug 19.

Jones BV, Sun F and Marchesi JR. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome. BMC genomics 2010 Jan 19;11:46.

Baker P, Kennedy J, Dobson ADW and Marchesi JR. Endoglucanase activities and growth of marine-derived fungi isolated from Haliclona simulans. J. Applied Microbiology. 2010 May;108(5):1668-1675.

Codling C, O’Mahony L, Shanahan F, Quigley EMM and Marchesi JR. A molecular analysis of fecal and mucosal bacterial communities in Irritable Bowel Syndrome. Digestive Diseases and Sciences. 2010 Feb;55(2):392-397


Claesson MJ, O’Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross P, O’Toole P. Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine. PLoS ONE. 2009 Aug 20;4(8):e6669.

Forbes C, O’Leary N, Dobson ADW and Marchesi JR. The contribution of “omic” based approaches to the study of enhanced biological phosphorus removal microbiology. FEMS Microbiology Ecology 2009 Jul;69(1):1-15.

Scanlan P., Shanahan F and Marchesi JR. Culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal and polypectomised individuals. FEMS Microbiology Ecology 2009 Aug;69(2):213-21.

Metagenomics and its application to human bacterial diseases. Marchesi JR. Invited chapter for book “Periodontal Medicine and Systems Biology” 2009.

Twomey K and Marchesi JR Swallowable Capsule Technology: current perspectives and future directions. Endoscopy 2009 41(4):357-362.

Turroni F, Marchesi JR, Foroni E, Gueimonde M, Shanahan F, Margolles A, van Sinderen D and Ventura M. Microbiomic analysis of the bifidobacterial population in the human distal gut. ISME Journal 2009 Jun;3(6):745-51.

Baker PW, Kennedy J, Dobson ADW and Marchesi JR. Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters. Marine Biotechnology 2009 Jul-Aug;11(4):540-7.

Kennedy J, Baker P, Walsh M, Mooij M, Rea MC, O’Connor PM, Piper C, Cotter P, Hill C, O’Gara F, Marchesi JR and Dobson ADW. Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans isolated from Irish waters. Marine Biotechnology 2009 11(3):384-96.


Kennedy J, Marchesi JR and Dobson ADW Marine Metagenomics: Strategies for the discovery of novel enzymes with Biotechnological applications from Marine Ecosystems. Microbial Cell Factories 2008. 7:27.

Jones BV, Begley M, Hill C, Gahan C, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proceedings of the National Academy of Science USA. 2008

Scanlan PD and Julian R. Marchesi JR. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture dependent and independent analysis. International Society of Microbial Ecology Journal 2008.

O' Mahony SM, Marchesi JR, Scully P, Codling C, Ceolho AM, Quigley EMM, Cryan J, and Dinan TG. Early life stress alters behaviour, immunity and microbiota: implications for irritable bowel syndrome and psychiatric illnesses. Biological Psychiatry. 2008.

Yap IKS, Li JV, Saric J, Martin F, Davies H, Wang Y, Wilson ID, Nicholson JK, Utzinger J, Marchesi JR, Holmes E. Metabonomic and Microbiological Analysis of the Dynamic Effect of Vancomycin-Induced Gut Microbiota Modification in the Mouse. J. Proteome Research 2008.

Scanlan PD, Shanahan F, Marchesi JR. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol. 2008 May 20;8:79.

Kennedy J, Codling CE, Jones BV, Dobson ADW and Marchesi JR (2008) Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Env. Micro. 2008. epub.

Scanlan PD, Shanahan F, Clune Y, Collins JK, O'Sullivan GC, O'Riordan M, Holmes E, Wang Y, Marchesi JR. Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol. 2008 10(3):789-798. PMID: 18237311.

Saric J, Wang Y, Li J, Coen M, Utzinger J, Marchesi JR, Keiser J, Veselkov K, Lindon JC, Nicholson JK, Holmes E. Species variation in the fecal metabolome gives insight into differential gastrointestinal function. J Proteome Res. 2008 7(1):352-360. PMID: 18052033.  


Jones BV, Marchesi JR. Accessing the mobile metagenome of the human gut microbiota. Mol Biosyst. 2007 3(11):749-758. PMID: 17940657.

Jones BV, Sun F, Marchesi JR. Using skimmed milk agar to functionally screen a gut metagenomic library for proteases may lead to false positives. Lett Appl Microbiol. 2007 45(4):418-420. PMID: 17897385.

Kennedy J, Marchesi JR, Dobson AD. Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Appl Microbiol Biotechnol. 2007 75(1):11-20. PMID: 17318533.

Moriarty J, Marchesi JR, Metcalfe A. Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: theory and practical application to genomic and metagenomic projects. BMC Bioinformatics. 2007 8:70. PMID: 17335566.

Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 2007 6(2):546-551. PMID: 17269711.

Jones BV, Marchesi JR. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods. 2007 4(1):55-61. PMID: 17128268.


Scanlan PD, Shanahan F, O'Mahony C, Marchesi JR. Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. J Clin Microbiol. 2006 44(11):3980-3988. PMID: 16988018.